The study of fungi and fungus-like organisms in irrigation ponds has applied interest since waterborne phytopathogens can disperse through the irrigation system to the crop roots. We tested the hypothesis that managing irrigation ponds to maintain high levels of biodiversity could entail agronomic benefits through the control of phytopathogens. The structure of assemblages of fungi and fungus-like taxa were characterized and compared using samples taken from two strata depths (superficial and deep). This was done in four management/water source pond groups of southeastern Spain: groundwater-fed ponds with submerged aquatic vegetation stands (untreated SAV ponds); groundwater-fed ponds submitted to low and high doses of copper sulfate, and ponds fed with recycled urban wastewater bearing intermediate doses of copper sulfate. Higher density and diversity of fungi, besides a singular assemblage composition, were found in untreated SAV ponds compared to treated ponds, particularly for samples taken in the deep stratum. Phytopathogenicity of the main phytopathogens detected (Pythium isolates) was generally low and rather unaffected by the type of pond management. However, much evidence from potential unsuitable hosts (submerged macrophyte species) and fungal composition (related to the presence of potential pathogen antagonists) suggests that managing ponds to preserve submerged vegetation might prove useful for controlling root rot diseases.