Understanding the spatial structure of populations at different scales can help reveal the processes controlling abundance and distribution. For species with a pelagic larval stage and highly mobile post-larval stage, such as the common cockle Cerastoderma edule, changes in spatial distribution from settlement through to juvenile stages are likely to occur at various spatial scales influencing the population dynamics observed. To record such changes a small-scale high-resolution field survey of C. edule post-larvae over an area of 60 × 80 m of tidal mudflat was conducted using a spatially-explicit staggered-nested design in the Dee estuary, UK. The survey was repeated three times from initial settlement in June 2011 to March 2012. Changes in spatial structure were described using Moran's I correlograms and prediction mapping, with analysis of correlations between cockle cohorts and sediment composition. At the first sampling event in June 2011, when initial settlement was occurring, post-larvae were highly aggregated in patches of 10–14 m in size and 16–20 m apart. By October 2011 the post-larvae had become more evenly dispersed with some small scale (<4 m) random patchiness and a gradient in post-larval density. This spatial structure was maintained into March 2012 but with increased patchiness. At settlement post-larval density showed no correlation with adult abundance or sediment mud content, but by October 2011 and March 2012 there was a strong positive correlation with adult abundance. Such changes in spatial structure, abundance and adult association after settlement show the likely importance of small scale (metres to tens of metres) processes on post-larval survival from predation and adult interactions, thereby potentially shaping adult distributions. Small scale patchiness in post-larvae can be created at settlement; however the distribution and association with adults change over time.