Almost all home aquaria contain substrate, either as intentional enrichment or for aesthetic purposes. For fishes, benefits of structural enrichment have been well considered, particularly in research and aquaculture settings. However, our understanding of the impacts of tank substrate as enrichment is limited. While substrate can induce foraging in some species, a major drawback is the potential of substrate to harbour elevated levels of waste and pathogenic bacteria. Here, we considered whether substrate as a form of environmental enrichment significantly altered water quality and bacterial presence in home aquaria. Water quality (temperature, oxygen, pH, TAN, unionised ammonia, nitrate, Ca2+, Na+, Mg2+ and K+) and bacterial presence (Pseudomonas spp.) were measured over two seven-week periods in stand-alone, tropical, freshwater tanks that simulated home aquaria. The following four enrichment conditions were considered: bare tanks, plastic plants, gravel substrate or sand substrate. The addition of both gravel and sand resulted in increased pH, concentrations of total ammonia nitrogen and nitrate. Substrate was also associated with a greater Pseudomonas presence. Decreased pH alongside an increased concentration of ions were also observed depending on the time of year. In conclusion, enrichment type affected the water quality of home aquaria, with further research needed on the role of the tank biome in fish welfare.