Hopkins used sprung rhythm, which was his version of accentual verse. In accentual verse, while the number of stressed syllables in a line is regular, the length of the feet (the number of unstressed syllables between stressed syllables) varies. Much of the time in Hopkin's poems, it's fairly evident which syllables should be stressed, but when it wasn't, he put acute accents on stressed syllables and grave accents on unstressed syllables to aid the reader.
ADDED: Let me add to this answer. Hopkins' manuscripts used a number of other strange symbols that indicated how the poem was supposed to be read. The editor (Robert Bridges) reduced these to acute accents, that indicated the syllable was the main stress in a foot, and grave accents in words like charmèd, where it indicates the ending -ed should be its own syllable, so the word is not the one-syllable charm'd the way it usually is pronounced.