Drastic losses of wetland habitats across North America over the past century have resulted in population declines of many marsh birds therefore emphasizing the need for proper management of remaining wetlands for the conservation of marsh birds. Our objective was to evaluate the probability of site occupancy of secretive marsh birds in Iowa in response to habitat variables at multiple scales. We conducted call-broadcast surveys for eight species of marsh birds at wetlands in Iowa from 16 May–15 July 2009 and from 20 April–10 July 2010. We utilized occupancy models in Program MARK to estimate site occupancy probability based on habitat covariates for four species with the most detections (Pied-billed Grebe [Podilymbus podiceps], Least Bittern [Ixobrychus exilis], Virginia Rail [Rallus limicola], and Sora [Porzana carolina]). Wetland size had a positive effect on site occupancy for Least Bitterns, water depth positively affected site occupancy for Pied-billed Grebes and Least Bitterns, and percent cover of cattail positively affected site occupancy for Virginia Rails. Knowing habitat associations of secretive marsh birds in Iowa will allow us to provide guidance on wetland restoration and management decisions that will aid the conservation of these birds.