The Eurasian otter is a wide-ranging semi-aquatic mammal that underwent a significant population decline in the last century, leading to local extinctions, reduction and fragmentation of populations. The individuals of populations exposed to both external and internal stress may present the inability to produce a specific developmental outcome, generating developmental ‘noise’ (developmental instability (DI)). Factors contributing to DI include inbreeding depression, population bottlenecks, habitat loss and exposure to pollution. We analysed fluctuating asymmetry (FA) as a proxy of DI in two European otter populations that experienced a major decline in the 1990s. Using three-dimensional geometric morphometrics methods on skull samples of otters from the UK and Sweden, we compared the degree of FA both between populations before, during and after the decline. We found a higher FA in the UK populations compared with Sweden. The level of asymmetry differed significantly over time only in the UK population, where it was higher during the decline phase. FA in the UK populations can be attributed to the specific impact of polychlorinated biphenyls pollution that caused a bottleneck. More generally, our study suggests that habitat loss, pollution and limited gene flow may contribute to DI in declining otter populations, highlighting the need for continued investigation to identify and quantify the specific stressors behind this trend in local populations.