In 2009, CBF filed suit against the US Environmental Protection Agency (EPA) for its failure to finalize a total maximum daily load (TMDL) ruling pursuant to the Clean Water Act that would restrict water pollution from farms, land development, power plants and sewage treatment plants.

[10] In the 2010s and 2020s, CBF was involved in lawsuits to stop the relicensing of the Conowingo dam, a hydropower plant that generates emission-free electricity to power 165,000 homes.

[11][12] In 2020 CBF filed a lawsuit against EPA for its failure to require the states of New York and Pennsylvania to reduce pollution in the bay.

[13] In 2001, CBF moved from a walkable downtown location in Annapolis to a new headquarters building, the Philip Merrill Environmental Center, about 5 miles (8 km) outside of town.

The foundation's choice for a new headquarters site symbolizes a dilemma of the modern environmental movement: how to be connected to the environment without despoiling it.

In this case, the enlarged footprint of employees and visitors forced to drive to the building was offset by its reduced imperviousness compared to the former inn, use of recycled materials, re-use of wastewater on-site, and use of composting toilets.