Fungicides are regularly applied in horticultural production systems and may migrate off-site, potentially posing an ecological risk to surface waterways. However, few studies have investigated the fate of fungicides in horticultural catchments. This study investigated the presence of 24 fungicides at 18 sites during a 5-month period within a horticultural catchment in southeastern Australia. Seventeen of the 24 fungicides were detected in the waterways, with fungicides detected in 63% of spot water samples, 44% of surface sediment samples, and 44% of the passive sampler systems deployed. One third of the water samples contained residues of two or more fungicides. Myclobutanil, trifloxystrobin, pyrimethanil, difenoconazole, and metalaxyl were the fungicides most frequently detected, being present in 16-38% of the spot water samples. Iprodione, myclobutanil, pyrimethanil, cyproconazole, trifloxystrobin, and fenarimol were found at the highest concentrations in the water samples (> 0.2 μg/l). Relatively high concentrations of myclobutanil and pyrimethanil (≥ 120 μg/kg dry weight) were detected in the sediment samples. Generally the concentrations of the fungicides detected were several orders of magnitude lower than reported ecotoxicological effect values, suggesting that concentrations of individual fungicides in the catchment were unlikely to pose an ecological risk. However, there is little information on the effects of fungicides, especially fungi and microbes, on aquatic ecosystems. There is also little known about the combined effects of simultaneous low-level exposure of multiple fungicides to aquatic organisms. Further research is required to adequately assess the risk of fungicides in aquatic environments.