The aim of the research is to improve approaches to assessing and predicting the environmental sustainability of innovative enterprises (IEs) for their sustainable development. The concept of environmental sustainability is defined, and the mechanism for managing it at IEs is developed. To implement the system of methods, models, principles, functions, actions, stages, and operations of the proposed management mechanism of the IE’s environmentally sustainable development, intelligent environmental monitoring, and a set of indicators for assessing and forecasting the status of an IE’s environmental sustainability were developed. It is proposed to evaluate the statuses of environmental sustainability of IEs on the basis of expert assessments of indicators and the developed scoring system and to forecast them using Markov chains described by the system of Kolmogorov differential equations and the corresponding system of algebraic equations. The proposed methodology was tested on the environmental sustainability analysis of Enzym Company (Lviv, Ukraine) in 2017–2021. The results of the study allow us to objectively assess the statuses of environmental sustainability of the enterprise and determine their probability, as well as its directions of sustainable development and ways of introducing innovative eco-technologies.