Ponds in agricultural landscapes are often used by amphibians as breeding habitat. However, the characteristics of agricultural ponds and especially the surrounding area are usually said to be suboptimal for many amphibian species. Using suboptimal habitats might allow a species’ survival and reproduction, but can have negative consequences at the individual and population level. In the present study, we investigated Palmate Newt (Lissotriton helveticus) populations from an intensive wine-growing region in southern Germany and compared them with populations located in a nearby forested area in terms of biometric traits, age and genetic structure. By analyzing over 900 adult newts from 11 ponds, we could show that newts reproducing in forest ponds were larger than newts reproducing in agricultural ponds. We did not find differences in the newt age and growth rate between habitat types. Therefore, differences in the body size of newts might already existed in larvae and/or juveniles, what might be related to a lower habitat quality for larvae and/or juveniles in the agricultural landscape. Body mass, body condition and sexual dimorphic traits (length of the caudal filament and max. height of the tail) correlated with body size, but no additional effect of the habitat type was found. The analysis of microsatellites revealed a higher genetic diversity in forest ponds. However, no clear sign of inbreeding was observed in any agricultural population, suggesting some degree of gene flow between them. We conclude, that agricultural ponds can be suitable habitats for the Palmate Newt and that conservation effort should aim to preserve them. The observed effects on body size indicate the need to increase the quality of the aquatic and terrestrial habitat for early life stages of this newt species in agricultural landscapes.