The Boundary Waters chronicles the unfolding and sometimes comic relationship between Raymona Washington Goldberg, an African American woman adopted as an infant by Jewish parents during a Freedom Ride in the 1960's and Matthew Pierson a gay man who geographically lives in Minneapolis but psychically inhabits a world of romantic fantasies. She spends her time barricaded in her Upper East Side Apartment in New York City, afraid to be contaminated by the stories lurking in the most common circumstances. Matthew distracts himself with romantic stories in which he becomes entangled. Their phone conversations provide a hygienic boundary through which Raymona experiences the world and Matthew has an audience.

Their relationship takes a dramatic turn when Matthew entangles himself with three other gay men who are going to The Boundary Waters in Minnesota. One of the men is at the end stage of AIDS. Matthew is quite suddenly captured in an adventure in which wishful happy endings lose all meaning.

Not only does the boundary between Raymona and Matthew start shifting, but both characters begin exploring the carefully guarded boundaries in their own lives. Their stories interact in a kind of synchrony as they stumble through the comedy and heartbreak of the human condition.