Despite the recent rapid decline of many grassland bird species, the relative importance of habitat configuration to population persistence is unclear. We used Southeastern American Kestrels Falco sparverius paulus in north-central Florida as a model system to explore the relative influence of landscape structure components on site occupancy patterns at two spatial scales, and for two different time periods. We focused on the dynamic processes of site-level population expansion or contraction. We modelled the occupancy of 131 American Kestrel nest boxes with Bayesian state-space dynamic occupancy models that considered both the partially observed process of true occupancy and the probability of detection of occupancy. We used reversible jump Markov chain Monte Carlo (RJMCMC) algorithms to identify variables that described the continued occupancy of nest boxes, or φ, and the probability of colonisation of nest boxes between time periods, or γ3. Changes in open habitat patch isolation at a fine scale, as estimated by the variability of nearest neighbour distance, predicted site colonisation between decades, and patch shape variability was related to φ during the early time period (1992-93). We found no strong effects of landscape structure on φ during the later time period (2008-2010). We also found no evidence for effects of loss of open habitat on box occupancy or colonization. Our results indicate that continued habitat fragmentation would be deleterious for this threatened subspecies. Additionally, certain land cover management practices recommended for the Florida sandhills, such as frequent low-intensity controlled burns, will likely help conservation attempts.