The study assessed the clinical utility of an invented spelling tool and determined whether invented spelling with linguistic manipulation at segmental and supra-segmental levels can be used to better identify reading difficulties. We conducted linguistic manipulation by using real and nonreal words, incorporating word stress, alternating the order of consonants and vowels, and alternating the number of syllables. We recruited 60 third-grade students, of which half were typical readers and half were poor readers. The invented spelling task consistently differentiated those with reading difficulties from typical readers. It explained unique variance in conventional spelling, but not in word reading. Word stress explained unique variance in both word reading and conventional spelling, highlighting the importance of addressing phonological awareness at the supra-segmental level. Poor readers had poorer performance when spelling both real and nonreal words and demonstrated substantial difficulty in detecting word stress. Poor readers struggled with spelling words with double consonants at the beginning and ending of words, and performed worse on spelling two- and three-syllable words than typical readers. Practical implications for early identification and instruction are discussed.