We study minimal time strategies for the treatment of pollution in large water volumes, such as lakes or natural reservoirs, with the help of an autonomous bioreactor. The control consists of feeding the bioreactor from the resource, with clean output returning to the resource with the same flow rate. We first characterize the optimal policies among constant and feedback controls under the assumption of a uniform concentration in the resource. In the second part, we study the influence of inhomogeneity in the resource, considering two measurement points. With the help of the Maximum Principle, we show that the optimal control law is non-monotonic and terminates with a constant phase, in contrast to the homogeneous case in which the optimal flow rate decreases with time. This study allows decision makers to identify situations in which the benefit of using non-constant flow rates is significant. © 2011 Elsevier Ltd. All rights reserved.