Environmental water allocation is considered an essential management tool for the rehabilitation aquatic environments within the Murray-Darling Basin (MDB). Carp are a widespread and abundant alien pest fish species whose populations may expand rapidly following flooding. Hence, there is concern that environmental watering may lead to increases in Carp populations. This paper illustrates the utility of a carp population model to investigate carp population dynamics under a range of flow scenarios, including: natural floods; within-channel flows, targeted delivery to floodplains and wetlands and; flow sequences. Recommendations from this work include ensuring that: environmental flow objectives for native biota remain paramount; carp are managed as a coincident risk in conjunction with water management; carp management plans are developed and implemented for each carp ‘hotspot’ and major watering site; and there is monitoring of the response of carp populations. Case studies are presented for four habitat types in the lower MDB 1) terminal lakes, 2) floodplain redgum forest, 3) complex river channel system and 4) artificial floodplain inundation using a regulator. These case studies highlight the unique nature of outcomes, depending on site, time, location and management/flow regime.