The studies on the variation of acoustic communication in different species have provided insight that genetics, geographic isolation and adaptation to ecological and social conditions play important roles in the variability of acoustic signals. The dolphin whistles are communication signals that can vary significantly among and within populations. Although it is known that they are influenced by different environmental and social variables, the factors influencing the variation between populations have received scant attention. In the present study, we investigated the factors associated to the acoustic variability in the whistles of common bottlenose dolphin (Tursiops truncatus), inhabiting two Mediterranean areas (Sardinia and Croatia). We explored which factors, among 1) geographical isolation of populations, 2) different environments in terms of noise and boat presence and 3) social factors (including group size, behaviour and presence of calves), were associated to whistle characteristics. We first applied a principal component analysis to reduce the number of collinear whistle frequency and temporal characteristics, and then generalised linear mixed models on the first two principal components. The study revealed that both geographic distance/isolation and local environment are associated to whistle variations between localities. The prominent differences in the acoustic environments between the two areas, which contributed to the acoustic variability in the first principal component (PC1), were found. The calf’s presence and foraging and social behaviour were also found to be associated with dolphin whistle variation. The second principal component (PC2) was associated only to locality and group size, showing that longer and more complex tonal sound may facilitate individual recognition and cohesion in social groups. Thus, both social and behavioural context influenced significantly the structure of whistles, and they should be considered when investigating acoustic variability among distant dolphin populations to avoid confounding factors.