In my opinion, this is one of the best ecological accounting methodologies I've seen around (http://www.ecologistasenaccion.org/IMG/pdf/info_cuentas-ecologicas.pdf). Its is focused on transport, but it could be transferred to any sector. Unfortunately, the report is in Spanish.
I recommend the book Sustainability Accounting and Accountability by Jan Bebbington (the author recommended by Mohamed El-Haram) Jeffrey Unerman and Brendan O´Dwyer
Easy to digest and suitable for different levels of knowledge on the topic. I didn't read it fully yet, but I reckon that the most relevant part for you would be in chapter III, accounting for sustainable development within organizations. Section 13 focuses on environmental and social assessment in sustainable finance.
It depends on what you are looking for: micro-economic budgeting and accounting by enterprises or macro-economic national accounting. The latter is dealt with at the international level by the United Nations, which published various volumes on a System of Environmental-Economic Accounts (SEEA). For a critique of their approach you might consult an article of mine in the Review of Income and Wealth 2014, 60 (4) on 'Environmental-Economic Accounting: Progress and Digression in the SEEA revisions'.