This study assesses the effects of considering within-site habitat configuration when designing reserve networks. This attribute takes all its importance in situations where the long-term integrity of (within-site) habitat patches cannot be preserved without protecting their surrounding environment. We addressed this issue through the concrete problem of selecting a reserve network of natural peatlands in southern Québec, Canada. We used a reserve-selection algorithm that minimized the total number of peatlands to include within networks. The algorithm was constrained to include peatlands containing habitat patches that met specific size thresholds. Five habitat-clustering thresholds were used to set the eligibility of each site to the selection process. The resulting reserve networks were evaluated according to their representation efficiency and to the expected consequences for the Palm Warbler (Dendroica palmarum), an area and isolation-sensitive bird restricted to peatlands in southern Québec.Constraining the algorithm to include peatlands showing increasingly larger patches of habitats led to larger networks, both in terms of area and number of sites, and to networks composed of smaller sites. These effects increased with the representation target (i.e., the % of each habitat preserved). With respect to the Palm Warbler, selecting peatlands with larger patches of habitats had only an indirect effect on its site-occupancy pattern. Indeed, despite the fact that the probability of occurrence of the warbler was negatively correlated with the size of habitat patches, the habitat-clustering threshold influenced the incidence of the warbler mainly via its effect on the physical attributes of the selected networks – including the area, isolation level, and the number of selected sites. Because increasing the habitat-clustering threshold led indirectly to a greater regional availability of prime breeding habitats for the Palm Warbler, it mitigated the severe negative impact of an hypothetical alteration or destruction of non-selected peatlands. Our study thus emphasizes the importance of determining how the different factors describing within-site configuration are correlated with other intrinsic characteristics of the sites available to the selection process before opting for a site-selection strategy.