2.1. Study Design

A completely randomized design was used in setting up the aquaponics system comprising of four hydroponics systems in triplicates. A total of 12 fish tanks were stocked with O. niloticus fingerlings randomly. Grow beds were blocked to ensure each fish tank empties its water into specific hydroponic system, and thereafter, the water was recycled back to the fish tank. One leafy vegetable crop, B. oleracea (Kale), was grown on nine growing beds in each of the three media based hydroponic systems and along the 12 polyvinyl chloride (PVC) pipes in the raft system.

2.2. Design of the Aquaponics System

The system was set-up at the innovation center for bioresources greenhouses at Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya (Figure 1). The system comprised of 12 fish tanks, nine media grow beds, and 12 nutrient pipes for the raft system in 12 independent units to ensure the independence of the results obtained from each treatment. For the media-based aquaponics system each unit had one 1150 mm long × 1365 mm diameter PVC cylindrical tank (1100 L) that served as an aquaculture tank, one 1420 cm × 1000 cm × 410 cm PVC loft tank (500 L) that served as media/plant grow bed, one 860 mm × 920 mm PVC cylindrical tank (500 L) that served as a sunk/collection tank placed in a hole dug below ground, and a 5-horsepower Thermoplastic Submersible Pump to pump the water from the sunk tank back to the fish tank. The system was also fitted with an air compressor for aeration. The media beds were filled with three selected medias, that is, pumice, perlite, and charcoal such that each media filled three beds.

For the raft-based aquaponics system each of unit had one 1150 mm long × 1365 mm diameter PVC cylindrical tank (1100 L) that served as an aquaculture tank, four 6 m length × 150 mm diameter PVC high density pipes that served as nutrient pipes for growing the crops, one 860 mm × 920 mm PVC cylindrical tank (500 L) that served as a sunk/collection tank, and a 5-horsepower Thermoplastic Submersible Pump to pump the water from the sunk tank back to the fish tank. The plants were grown in plastic netted pots (80 mm radius × 120 mm height) containing medium duty foam cushion (sponge) of 23 kg m⁻³ density with an indentation load deflection (ILD) of 30.5. These netted pots were fitted to the nutrient pipes with holes from top at spacing of 150 mm from each other. The water flowrate through the aquaponics system was maintained at 8 L min⁻¹.

2.3. Stocking the Fish Tank and Evaluation of Fish Growth

Nile tilapia fingerlings with average length and weight of 3.03 ± 0.18 cm and 28.25 ± 2.95 g, respectively, were sourced from Makindi fish farm, Thika, Kenya. The total number of fingerlings used were 1200 fingerlings stocked at 1 fingerling/10 L of water resulting to 100 fingerlings per tank. Feeding was done twice daily in the morning (0800 h–1000 h) and evening (1600–1800 h) to satiation during the fish culture period of 22 weeks. The fish feeds used were sourced from a commercial feed company (Unga Group PLC, Nairobi, Kenya) and it included stater extruded crumble with 40% crude protein (CP) for the first 1 month, pregrower feeds with 35% CP (2 mm floating pellets) for the second and third month, grower feeds with 35% CP (3 mm floating pellets) for the fourth and fifth month, and finally the finisher feeds with 30% CP (4 mm floating pellets) for the sixth month.

Nondestructive sampling of 10 fish from each tank was done fortnightly to estimate fish growth parameters the study period. Sampling was done using a hand-held fishing net and the fish samples placed in a bucket containing fresh water and taken to the laboratory to obtain the growth data (weight and length). The fish was weighed using a Dune Compact Balance (Adam Scales and Balances). While the length was obtained using an electronic digital caliper (Neiko 01407). The weight and length data were then used to estimate the body weight gain (BWG) and specific growth rate (SGR) of the fish. The calculation of the growth performance parameters was done according to the formulae described in the methodology given in the supporting information (Supporting Information: File S1).

2.4. Growing the Crops in Hydroponics System

Growth performance of B. oleracea in various hydroponic media within the aquaponics system was evaluated focusing on pumice, perlite, charcoal, and a raft system. Growth performance of the crops was monitored by taking data on above ground height of the crop, diameter at ground level, leaf index, increase in length and width of a tagged leaf, and length of tap root. These data were collected on weekly basis until the crop matured (2 months). Plant tissue analysis was done using published dry-ash (PDA) method [24]. At crop maturity, representative samples of B. oleracea were harvested from each hydroponic medium. The samples included both aboveground biomass (leaves and stems) and roots, although the leaves were primarily focused on for nutritional analysis. The collected plant tissues were thoroughly washed with distilled water to remove any adhering debris. Following washing, the samples were blotted dry and then oven-dried at a consistent temperature of 60–70°C until a constant weight was achieved. Once dried, the plant tissues were ground into a fine powder using a grinder to ensure homogeneity across the samples. For moisture content determination, a portion of the fresh tissue was weighed before and after drying. The difference in weight, expressed as a percentage of the fresh weight, provided the moisture content. For ash content measurement, a known weight of the dried, ground sample was placed in a crucible and incinerated at high temperatures (500–600°C) in a muffle furnace (Thermo Fisher Scientific) until all organic matter was burned off. The remaining inorganic ash was then weighed, and the ash content was calculated as a percentage of the original sample weight.

Crude fiber analysis was conducted by subjecting the ground sample to a series of acid and alkaline digestion processes, which broke down the digestible components and left behind the indigestible fiber. The remaining fibrous material was dried and weighed to determine the crude fiber content, expressed as a percentage of the original dry weight. CP determination was performed using the Kjeldahl method, where the sample was digested in concentrated sulfuric acid to convert nitrogen into ammonium sulfate. The digest was then neutralized with alkali, and the released ammonia was distilled and titrated to calculate the nitrogen content, which was then multiplied by a conversion factor to estimate the CP percentage. For crude lipid extraction, the lipids were extracted from the ground sample using a solvent extraction method with petroleum ether in a Soxhlet apparatus (Thermo Fisher Scientific). After extraction, the solvent was evaporated, leaving behind the lipid residue, which was weighed to determine the crude lipid content as a percentage of the sample weight.

2.5. Determining the Water Quality Parameters

Water quality parameter including temperature, dissolved oxygen (DO) levels, salinity, and pH were measured daily in each system at the fish tank and at the reservoir tank and maintained within acceptable limits for tilapia culture during the entire experimental period [25]. The water temperature and DO water levels were taken using YSI-550A multiparameter water quality meter, the water salinity was measured with a PAL-06S refractometer (Atago Company), and the pH by OxyGuard pH meter. For the chemical parameters of the culture water, 20 mL water samples from the fish tanks and the hydroponics system were collected and used to analyze the concentrations of total inorganic carbon (TIC), total nitrates (TN), and total suspended solids (TSSs) in triplicates from each system biweekly according to the standard methods for evaluation of water and wastewaters referred by Danish Standard Methods DS 224 (1975) [26, 27].

2.6. Data Collection and Analysis

3.1. Fish Growth Performance

The results of the growth performance of O. niloticus reared in the four aquaponics systems is presented in Table 1. At the end of the experiment, all the growth parameters were affected significantly by the choice of hydroponic unit. The SGR and BWD were highest in perlite and pumice medium and lowest in raft system (p < 0.05). The survival was above 90% in all the treatments. The feed conversion ratio (FCR), feed efficiency ratio (FER), and condition factor (CF) followed a similar pattern as the other growth indices with perlite and pumice having the highest and raft system resulting to lower indices. The biweekly fish growth curves are shown in Figure 2. The average final length of the fish varied significantly depending on the medium used (F = 85.61, p < 0.05), time (F = 105.34, p < 0.05), and intercept (F = 23.76, p < 0.05). Fish grown in the perlite medium exhibited the greatest increase in length, reaching an average final length of 29.14 ± 1.79 cm. This was followed by fish grown in the charcoal and pumice medium which also supported substantial growth, with fish reaching an average final length of 28.92 ± 1.42 and 28.32 ± 1.67 cm, respectively. In contrast, the raft system resulted in the least growth, with fish reaching an average final length of 23.50 ± 1.02 cm. Similar trends of growth performance were observed in the weight of the fish across the different media. The average final weight of the fish varied significantly depending on the medium used (F = 113.27, p < 0.05), time (F = 97.38, p < 0.05), and intercept (F = 18.62, p < 0.05). Fish grown in the perlite medium reached the highest final average weight of 440.43 ± 12.38 g. The pumice and charcoal medium also supported significant weight gain, with fish achieving an average final weight of 438.45 ± 10.61 and 432.85 ± 12.14 g, respectively. The raft system, consistent with the results observed for length, resulted in the lowest weight gain, with fish reaching an average final weight of 382.77 ± 8.36 g.

3.2. Plant Growth Performance

The results highlighted significant variations in plant growth (p < 0.05) and nutritional quality (p < 0.05) across these media, with pumice standing out as the most effective medium in supporting plant growth (Table 2). Plants grown in pumice exhibited the highest total biomass among all media (F = 13.86, p < 0.05). Specifically, the average dry weight of these plants was 18.16 ± 3.51 kg, while the fresh weight reached 23.44 ± 3.94 kg. Additionally, plants in pumice achieved the greatest average crop length of 79.56 ± 5.17 cm, reflecting robust vertical growth (F = 24.73, p < 0.05). The stem diameter and taproot length of these plants were also superior, measuring 3.03 ± 0.13 mm and 4.82 ± 0.64 cm, respectively. In terms of nutritional quality, plants grown in pumice exhibited the highest CP content, which was 9.51 ± 0.27% by mass (F = 17.59, p < 0.05). While other media such as charcoal and perlite also facilitated substantial growth, they did not match the performance of pumice across all measured parameters. Charcoal, for example, supported a dry weight of 17.47 ± 4.26 kg and a crop length of 78.94 ± 4.20 cm, both slightly lower than pumice. Perlite, on the other hand, yielded the highest crude lipid content at 7.94 ± 0.63% by mass, but lagged behind in overall biomass and structural measurements. The raft system was the least effective, producing the lowest growth rates and nutritional values.

3.3. Water Quality Analysis and Waste Removal Efficiency

The physiochemical water quality parameters were within the recommended ranges and are provided in Supporting Information 2: Table S1. Results demonstrated that the charcoal medium was the most effective at reducing TAN levels (Figure 3A). Specifically, TAN concentration in the charcoal system decreased from 13.59 ± 2.61 mg L⁻¹ in the fish tank to 4.47 ± 1.04 mg L⁻¹ in the sump tank, corresponding to a 67.1% reduction. This significant decrease highlights the superior capacity of charcoal for ammonia removal. In comparison, the pumice medium achieved a 50.0% reduction in TAN, with levels dropping from 9.84 ± 1.77 to 4.92 ± 0.96 mg L⁻¹. The perlite system exhibited a similar reduction of 49.7%, with TAN levels decreasing from 11.49 ± 2.82 to 5.78 ± 1.65 mg L⁻¹. The raft system was the least effective, reducing TAN by only 30.7%, from 10.63 ± 2.17 to 7.37 ± 2.01 mg L⁻¹.

The reductions in TIC concentrations were relatively small across all media, indicating a limited impact on carbon capture (Figure 3B). In the charcoal system, TIC levels decreased by 6.3%, from 0.63 ± 0.05 mg L⁻¹ in the fish tank to 0.59 ± 0.03 mg L⁻¹in the sump tank. The pumice medium showed a 4.9% reduction, with TIC levels dropping from 0.61 ± 0.10 to 0.58 ± 0.83 mg L⁻¹. Similarly, perlite and raft systems exhibited TIC reductions of 4.8% and 5.2%, respectively. The minimal reductions in TIC across all media suggest that carbon capture was not significantly influenced by the choice of medium, with only slight variations observed. Among the media tested, pumice exhibited the highest TSS retention capacity, with 25.9% reduction in TSS levels, decreasing from 72.84 ± 13.85 mg L⁻¹ in the fish tank to 44.92 ± 9.43 mg L⁻¹ in the sump tank (Figure 3C). Charcoal and perlite had TSS reductions of 14.0% and 10.2%, respectively. The raft system, which showed the lowest reduction in TSS levels at 9.6%, decreased from 54.63 ± 7.36 to 49.37 ± 5.82 mg L⁻¹.

4.1. Fish Growth Performance

The fish growth data indicated that the type of medium significantly impacted both the length and weight of the fish. Fish reared in perlite exhibited the greatest growth, followed by those in charcoal and pumice substrates, while those in the raft system showed the least growth. The superior performance of perlite may be attributed to its light-weight structure, which enhances water aeration and reduces the buildup of organic waste, thereby, maintaining a healthier environment for fish [16, 17, 28]. This finding aligns with previous studies that have shown the importance of substrate selection in aquaponics systems for sustaining optimal water quality and enhancing fish growth [8, 13, 29]. The hydroponic medium serves as a substrate for plant roots and plays a critical role in nutrient uptake and water quality management [3, 7, 17]. However, the raft system’s lower performance could be linked to its limited capacity for solid waste removal. As the results indicate, the raft system was less effective at reducing TAN and TSS compared to the other media. Elevated TAN levels can be toxic to fish, leading to stress and reduced growth rates [18, 28]. The inefficiency in waste removal could have contributed to the suboptimal conditions observed in the raft system, underscoring the necessity of integrating additional filtration mechanisms when employing such systems.

4.2. Plant Growth Performance

The growth performance of B. oleracea varied significantly across the media, with pumice proving to be the most effective substrate. Plants grown in pumice exhibited the highest biomass and structural measurements, including crop length, stem diameter, and taproot length. These results suggest that pumice’s porous structure provides an optimal balance of water retention, aeration, and nutrient availability, promoting robust plant growth [16, 30]. The high surface area of pumice facilitated effective colonization by beneficial microorganisms, enhancing nutrient cycling and plant nutrient uptake. Charcoal and perlite also supported substantial plant growth, though they did not match pumice’s overall performance. Charcoal’s ability to adsorb organic compounds and excess nutrients likely contributed to maintaining water quality and supporting plant growth [14, 15, 31]. Perlite, while offering excellent aeration, seemed to fall short in water retention compared to pumice, which could explain its lower biomass production. Interestingly, perlite’s ability to promote fish growth did not translate into the same level of effectiveness for plant growth, highlighting the need to balance substrate selection based on specific system goals. The raft system, consistent with its performance in fish growth, was the least effective for plant growth. The lower biomass and nutritional content observed in plants grown in the raft system could be attributed to insufficient nutrient absorption, as the system’s design may not have facilitated efficient root contact with nutrients.

4.3. Water Quality and Waste Removal

Water quality parameters, particularly TAN and TSS, are critical indicators of the health and sustainability of aquaponics systems. Total ammonia nitrogen (TAN) concentration is a critical indicator of nitrogen waste in aquaponics systems, reflecting the effectiveness of ammonia removal. The study found that charcoal was the most effective medium for reducing TAN levels, followed by pumice and perlite. Charcoal’s adsorption capabilities likely played a crucial role in ammonia removal, which is essential for maintaining nontoxic conditions for fish and optimizing nutrient availability for plants. The effectiveness of charcoal for ammonia removal can be attributed to its high surface area and porous structure, which facilitate the adsorption of ammonia molecules [29, 31, 32]. These studies indicate that optimizing parameters such as contact time, pH, and modification with iron can significantly improve ammonia removal rates. The adsorption process involves the interaction between ammonia molecules and the surface of charcoal [33]. The porous nature of charcoal allows for many active sites where ammonia can adhere. Factors such as the chemical treatment of the charcoal, the physical characteristics of the charcoal source, and operational conditions (like pH and contact time) influence the overall effectiveness of ammonia removal [11, 17, 32, 34].

The TIC concentration in all the four aquaponics systems showed relatively small reductions, ranging from 4.8% to 6.3%, with charcoal achieving the highest reduction. TIC is primarily available as bicarbonates (HCO₃⁻) and carbonates (CO₃²⁻) and plays a vital role in aquaponics as a carbon source for photosynthesis in plants and microorganisms [35–37]. Although the reductions were minimal, this mechanism likely contributed to the observed decrease, consistent with findings by Lenz et al. [36], who reported limited TIC uptake in closed-loop aquaponics systems due to suboptimal carbon availability for plant absorption. Processes such as microbial activity, plant uptake, chemical precipitation, and water–air gas exchange influence TIC dynamics in aquaponics systems [37, 38]. Plants in hydroponic systems utilize dissolved inorganic carbon during photosynthesis, converting it to organic compounds, though this mechanism has limited impact in closed-loop systems [39, 40]. Charcoal media in this study had slightly better TIC reduction that can be attributed to its high porosity and surface area which fostered microbial colonization [41, 42]. Microorganisms aid TIC reduction by converting CO₂ and HCO₃⁻ into biomass through autotrophic processes [37]. These results are consistent with findings by Wong et al. [42] and Toafik, Qurohman, and Akhlasa [43], who noted biochar’s role in enhancing microbial activity and nutrient cycling.

Pumice, while less effective in TAN reduction, excelled in TSS retention, indicating its potential as a dual-function medium for both biofiltration and physical filtration. Other studies have demonstrated that pumice, either used alone or in combination with other substrates like sand or scoria, has the ability to effectively reduce TSS from various types of wastewaters, including dairy and tannery effluents [16, 30, 44]. The effectiveness of pumice in TSS reduction can be attributed to several mechanisms, including sedimentation, filtration, and adsorption. Its porous structure allows it to trap particles effectively, while its chemical properties may facilitate interactions that enhance solid removal [14, 45]. However, it has also been shown that, the removal efficiency can vary based on factors like hydraulic retention time, the size of pumice particles, and the presence, type, or density of vegetation [30, 46]. The raft system’s minimal impact on both TAN and TSS levels further highlights its limitations in waste management. This finding emphasizes the need for integrating additional filtration solutions when using raft systems, particularly in small-scale setups, where space and resource limitations might exacerbate waste management challenges.