The fungal disease chytridiomycosis has globally caused massive declines and even extinctions of amphibian populations. To date, no measures to control chytridiomycosis in natural amphibian populations exist. We propose manipulation of the aquatic environment as a measure to increase the chances of amphibians to survive in nature in the presence of chytridiomycosis, by limiting the disease’s impact on the amphibian populations. This proposal is based on our recent finding that microscopic aquatic organisms (“micropredators”) can ingest the chytrid fungus and reduce the number of infected amphibians. Here, we aim at identifying the aquatic parameters that determine the abundance and composition of the aquatic micropredator community. We will apply this knowledge to steer micropredator communities such that we can reduce the impact of chytridiomycosis on the amphibian community. If successful, this would open unprecedented perspectives for the management of wildlife diseases in situ.