Hi Clara,
Thanks for your question! I first want to make sure we are using some key terms the same way because there is an important distinction between hearing sounds and discriminating between sounds. Technically, whether or not a student can “hear” a sound refers to hearing acuity. For example, someone with a hearing loss may have difficulty hearing phonemes such as /f/ or /th/ because these are relatively low-intensity, high-frequency speech sounds that can be hard to detect. Without proper amplification or contextual support, the /f/ in fit may not be heard clearly, causing the word to sound more like it.
I suspect the difficulty you are describing is more related to phoneme discrimination than hearing itself. In other words, the student may hear the sounds adequately but struggle to mentally distinguish or represent them accurately. For example, a student may perceive the word peach as beach, confusing the two initial consonant phonemes. In this case, making the sounds louder would not necessarily help any more than it would help a native English speaker accurately repeat unfamiliar sounds and words from another language. The underlying difficulty lies within the student’s phonological processing system rather than the volume of the sounds themselves.
To your actual question, I am not aware of any assessments that provide the level of granularity needed to identify which specific phonemes a student can or cannot consistently discriminate. And, as you pointed out in your question, this can become especially complicated because a student may know a sound-symbol correspondence conceptually while still inconsistently perceiving or discriminating the sound during reading and writing tasks.
That being said, I do think the type of informal observation you are already doing during intervention is likely one of the most useful approaches. When students repeatedly substitute the same sounds during spelling, word reading, or dictation, those patterns can reveal which phoneme contrasts may be unstable for them. I would probably begin by informally tracking which sound confusions occur most often and then look for patterns among those sounds.
Students are most likely to confuse phonemes that share articulatory properties. Consonants that share two of the three major distinctive features (voice, place, and manner) are often more difficult to discriminate from one another than sounds that differ substantially. For example, a student who confuses she and see may specifically struggle distinguishing /sh/ and /s/, which differ primarily by place of articulation while sharing voicing and manner. Similarly, a student who confuses bat and pat may be struggling to distinguish voicing contrasts.
With this in mind, it may help to create a small inventory of potentially difficult phoneme contrasts for a student and probe those contrasts intentionally during intervention. Minimal pairs (pairs of words differing by only one phoneme) can be especially useful for this purpose. Ultimately, you would want the student to accurately hear, identify, and spell the correct word from the pair. One way to help isolate phoneme discrimination from possible confusion with letter-sound correspondences would be to first show the student pictures representing both words in the pair and ask them to point to the word you say aloud before asking them to spell it. This can help determine whether the difficulty lies in perceiving the phoneme contrast itself or in connecting the sounds to print. Speech-language pathology resources often contain excellent minimal-pair word lists organized by distinctive features or phonological processes, and these materials can be very helpful even in reading intervention settings.
I would also keep in mind that phoneme discrimination difficulties can sometimes reflect language background or dialect differences rather than a processing weakness. Students are often more likely to struggle perceiving and producing phonemes that are not present or contrastive within their native language or dialect. In these cases, the issue may be less about a deficit and more about familiarity and experience with the sound system itself.
Most importantly, I would continue paying attention to the patterns you are already noticing during intervention and using these observations to tailor your instruction. Those organic observations are often much more informative than a single isolated test score because they show you how the student is processing sounds during authentic reading and spelling tasks!