Well, biogas production is in theory a pretty positive process, because you trap the methane and use it, instead of letting it escape into the atmosphere where it is a significant greenhouse cause. Burning methane does release carbon dioxide, but its greenhouse contribution is much less.
I'd say that the main negative impact of biogas is in its construction, as it can use significant amounts of cement, and/or other materials that need transport.
See this GTZ doc, the lest 3 pages are about environmental conditions and effects.
In addition to the environmental impact you should also consider the social impact. I seem to recall that early digester projects in rural India reduced the available energy resources for poor people. Once cow dung became a useful resource for those that owned the cows and could afford the digesters, it was no longer available to poor people as their main source of fuel for cooking. Also, given the high proportion of failed and abandoned digester projects I have come across, you would need to factor in the probability that the project will produce no benefit (by, for example, increasing the resources consumed in construction and reducing the estimated energy produced) and consider the possible negative impact on attitudes to improved sanitation, if that is the main driver for the project.
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