Waterborne diseases pose a significant risk in hydroponic crops, especially those caused by some species such as Fusarium, Pythium and Phytophthora. However, there is evidence of an increase in suppressiveness when using aquaculture effluents, as is the case with aquaponic systems. In this work, the incidence of diseases in hydroponic and aquaponic systems inside a greenhouse located in Seville (Spain) has been compared for two pathosystems: strawberry - Phytophthora cactorum - and tomato - Fusarium oxysporum f. sp. lycopersici (Fol). The results obtained show greater suppressiveness in early stages against P. cactorum in aquaponic systems. On the contrary, the suppressivity against Fol was higher in the hydroponic systems, although in this case a significant influence of the nutritional status of the plants was observed. This negatively affected the aquaponic systems. These findings open an interesting line for the use of biological control agents (BCA) from aquaponic systems for the control of plant diseases in hydroponic systems, avoiding the use of pesticides. This can have a negative effect on the health of consumers and the environment.