Simple Summary Between 2018 and 2022, we surveyed small mammals at 23 sites in Lithuania-meadows, commercial orchards and berry farms, kitchen gardens, homesteads and farms-with the aim to assess the proportion of shrews in the community and their diet using stable isotope analysis. We found that in these natural, agricultural, and commensal habitats, common (Sorex araneus) and pygmy (Sorex minutus) shrews were under-represented-having a proportion of 3.1%, less than a half that of the long-term average in the country. The diet of these two species was similar in both agricultural and commensal habitats. On farms and in orchards with intensive farming, there were no catches of shrews. Contamination by plant protection products and a lack of invertebrates, which are the main food of shrews, may be factors limiting their numbers in the agriculturally managed habitats. Two species of water shrews, Neomys fodiens and Neomys anomalus, were found for the first time in homesteads, including in outbuildings, and their diet requires further investigation. Shrews are a less studied group of small mammals than rodents. Between 2018 and 2022, we surveyed 23 sites in Lithuania, including natural and anthropogenic habitats, with the aim to assess the proportion of Soricidae in small mammal communities and their diet based on stable isotope analysis. The average representation of Soricidae was 3.1%, about half the long-term average in other habitats in the country. The highest proportions were in meadows and farmsteads, at 4.9% and 5.0% respectively. Shrews were not trapped on farms or in young orchards, and their relative abundance was very low in intensively managed orchards (0.006 individuals per 100 trap days). Neomys fodiens and N. anomalus were unexpectedly found in homesteads, including in outbuildings. Sorex araneus and S. minutus had similar diets. The trophic carbon/nitrogen discrimination factor between invertebrates and shrew hair was 2.74 parts per thousand/3.98 parts per thousand for S. araneus, 1.90 parts per thousand/3.78 parts per thousand for S. minutus in the orchards. The diet of N. fodiens and N. anomalus at the homesteads requires further investigation. We propose that the under-abundance of shrews may be due to contamination by plant protection products and a lack of invertebrates under intensive agricultural practices.