Logic programs with aggregates (LPA) are one of the major linguistic extensions to Logic Programming (LP). In this work, we propose a generalization of the notions of unfounded set and well-founded semantics for programs with monotone and antimonotone aggregates (LPAma programs). In particular, we present a new notion of unfounded set for LPAma programs, which is a sound generalization of the original definition for standard (aggregate-free) LP. On this basis, we define a well-founded operator for LPAma programs, the fixpoint of which is called well-founded model (or well-founded semantics) for LPAma programs. The most important properties of unfounded sets and the well-founded semantics for standard LP are retained by this generalization, notably existence and uniqueness of the well-founded model, together with a strong relationship to the answer set semantics for LPAma programs. We show that one of the D-well-founded semantics, defined by Pelov, Denecker, and Bruynooghe for a broader class of aggregates using approximating operators, coincides with the well-founded model as defined in this work on LPAma programs. We also discuss some complexity issues, most importantly we give a formal proof of tractable computation of the well-founded model for LPA programs. Moreover, we prove that for general LPA programs, which may contain aggregates that are neither monotone nor antimonotone, deciding satisfaction of aggregate expressions with respect to partial interpretations is coNP-complete. As a consequence, a well-founded semantics for general LPA programs that allows for tractable computation is unlikely to exist, which justifies the restriction on LPAma programs. Finally, we present a prototype system extending DLV, which supports the well-founded semantics for LPAma programs, at the time of writing the only implemented system that does so. Experiments with this prototype show significant computational advantages of aggregate constructs over equivalent aggregate-free encodings.