The aim of the study is to assess environmental, organizational, and economic implications for agriculture in municipalities with different share of the Natura 2000 network in Poland. Data on the distribution of Natura 2000 sites and natural management conditions in municipalities are derived from the General Directorate for Environmental Protection and the Institute of Soil Science and Plant Cultivation State Research Institute for 2018. Data on the features of the organizational potential of agriculture across municipalities were collected from the Agency for Restructuring and Modernisation of Agriculture. They were generated on the basis of applications for direct payments under the 2016 and 2021 campaigns submitted by 1345.2 and 1269.5 thousand farms, i.e., the beneficiaries of the 2014–2020 common agricultural policy (CAP), respectively. It was found that municipalities with a large and particularly large share of Natura 2000 areas, as compared to municipalities without such areas, were characterized by significantly worse management conditions and a more diverse landscape, as well as a larger share in agricultural area with extensive production characteristic of high nature value farmlands (HNVf) designated in Poland under the 2014–2020 CAP. Farms located in Natura 2000 areas, as compared to other farms, were characterized by a larger average agricultural area, as well as by lower labor inputs per 1 ha of agricultural area. They were characterized by lower total costs, including direct costs, which resulted in lower factor productivity and income per 1 ha of agricultural area. The conclusion was that they had less development opportunities.