Malaria, historically a significant health burden in temperate Europe, particularly in the low-lying marshy areas, is often poorly represented in discussions of health in the pre-modern Netherlands. Although malaria does not produce pathognomonic skeletal lesions, the haemolytic anaemia associated with repeated infection is thought to contribute to the development of cribra orbitalia, making population-level patterns in this non-specific skeletal marker informative for exploring past malaria burden. This study applied a spatial epidemiological approach, which investigated (1) the spatial distribution of cribra orbitalia prevalence across 28 archaeological medieval sites in the Netherlands, and (2) whether this distribution can be explained by underlying environmental features consistent with malaria transmission and historical mosquito density. Global Moran’s I revealed a significant positive spatial autocorrelation in prevalence. Local Indicator of Spatial Association (LISA) analysis confirmed this, identifying distinct High–High clusters in the Southwest and Low–Low clusters in the East of the Netherlands. However, linear regression models using broad-scale environmental variables failed to explain these spatial patterns. This likely reflects their inability to capture the specific ecology of the local malaria mosquito, Anopheles atroparvus, which preferentially breeds in brackish environments. Consistent with this interpretation, cribra orbitalia prevalence was significantly positively correlated with historical (1938) estimates of A. atroparvus density. The observed clustering and correlation with mosquito density suggest that malaria contributed to cribra orbitalia prevalence and may have been an important disease in certain regions of the medieval Netherlands; however, interpretation is constrained by small non-adult sample sizes as well as uneven preservation across the Netherlands.