Small-scale hydroponic and aquaponic crop production is increasingly common in urban areas of the US and growers have questions about which system and crops to use. Hydroponic nutrient solution contains water soluble nutrients, electrical conductivity (EC) is maintained between 1 and 3dSm−1, and target pH is between 5.5 and 6. In contrast, plants in aquaponic systems are fertilized by aquaculture effluent, which is characterized by lower EC (less than 1dSm−1) and a target pH near 7.2. Duplicate greenhouse trials were conducted between 2013 and 2015 to assess the growth, yield, quality, and potential gross returns of four crops – basil (Ocimum basilicum L.), kale (Brassica oleracea L.), chipotle pepper (Capsicum annuum L.), and cherry tomato (Solanum lycopersicum L.) – grown in a recirculating ebb-and-flow system with nutrient solution EC and pH levels commonly observed in hydroponic (high EC–low pH) and small-scale aquaponic (low EC–high pH) systems. Solution pH and EC, plant height, and leaf greenness data were collected regularly throughout crop growth, and yield and percent soluble solids (°Brix) data were collected at harvest. Crops grown in the high EC–low pH solution approached a greater final height, but relative growth rate was not different from the low EC–high pH solution. Leaf chlorophyll content, estimated from leaf greenness, was up to 37% lower in the low EC–high pH solution. Marketable yield of basil and kale was reduced by 44% and 76% in the low EC–high pH solution, respectively. Yield loss in tomato and pepper was less severe (<32%), but still significant. Observed yield reductions were greater than previous comparisons of floating-raft aquaponic and hydroponic systems, which demonstrates the importance of root to nutrient solution contact area and fertigation frequency when using low EC–high pH nutrient solution (e.g., aquaculture effluent). Differences may also suggest there are components of aquaponic solution not tested in this mechanistic study (e.g., organic metabolites and alternative nutrient forms or ratios) that may contribute to crop growth and yield in aquaponics. On a per plant basis, kale ($10.62) and cherry tomato ($9.16) grown in the high EC–low pH solution provided the greatest potential gross returns, but farm-scale net profit potential will depend on many factors including plant spacing and input costs.