In the nominal morphology of Modern Hebrew, the vowels [a] and [e] alternate with each other and syncopate in several contexts. These contexts have received separate phonological and/or morphological analyses in the past. The phonological analyses have yielded phonologically unnatural rules; the morphological analyses have turned to the unconstrained concept of stem-allomorphy. In the first part of this paper, a unifying account of these vocalic alternations is provided in the framework of CVCV-Phonology (Lowenstamm 1996), relating the contexts to one another. Specifically, it is proposed that some vowels are phonologically long, either lexically or through a rule of pretonic lengthening. In the second part of the paper, an alternation which resists the strictly phonological explanation is shown to follow from morpho-syntactic principles of derivation by phase (Embick 2010). While certain phonological processes apply whenever the domain of a category head is processed, only the merger of the head D triggers the realization of the underlying phonological string.