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Adverse transformations of protected areas (PAs) may be reflected in the PADDD conceptual framework: downgrading, downsizing and degazettment. Meanwhile, an urban environment is exposed to significant human impact, specific entanglement of stakeholders’ demands and exceptional variety of land-use conflicts. In this regard, a detailed structure of adverse transformations of two megapolises (Moscow and Saint-Petersburg) has been disclosed: 4th type (design of planned and proposed PAs), 8 subtypes and 15 levels of possible alterations. Spatial analysis of adverse transformations (PA4D) through QGIS mapping has been conducted on the basis of legislative acts with the attached raster images or coordinates of transformed areas. The imageries from open-source Google Earth Pro since 2005 have been harnessed to assess ecosystems’ differentiation in terms of PA4D. Negative transformations have affected about 53.8% of total area that was ever under protection in Moscow due to complicated history of legislative changes. Besides, positive transformations (PA4P) are considerably less spread than PA4D. The core contributor to PA4D in Moscow is downgrading, particularly a subtype of partial downgrading (60.3% of PA4D area), which is different from the downgrading of entire PA. The second most important constituent is related to low speed of proposed PAS’ design (22.8% of PA4D area). At the same time, Saint-Petersburg considerably differs from Moscow – almost all PA4D actions are due to extremely low speed of PAs’ design (only 15.2% of total area planned in 2008). Wetlands are considered as biotopes of the highest vulnerability to PA4D, but even remote forests’ parts are threatened by easing prohibitions on extensive recreation, primarily construction of permeable pavements. Hence, such almost complete absence of local governance leads to significant ramifications for providing ecosystem services. Although state-led system of PAs planning and management can report on formal extension of green infrastructure and PAs, in-depth spatial dynamic analysis unveils predominantly negative tendencies. The devised PA4D model may be implemented in the regional and international blueprints of environmental planning to design resilient cities that are able to retain well-being of citizens. Moreover, PA4D concept should be used to assess an effectiveness of government entities and need to facilitate a local interest.