Dead branches in a juniper could be due to a fungal blight of the affected shoot or from spider mites. Mites tend to brown the area slowly over time while shoot blights are more sudden. Root problems such as soggy soil conditions can also contribute to problems above ground.
Prune out the dead shoots just below where the living growth begins. Remove them from the area and rake up any fallen needles. When you water try not to get it on the foliage any more often than you have to. Drip irrigation is best but a sprinkler that is not run very often is okay too.
In late winter, fertilize the plant with a light application of turf fertilizer and water it in well to promote new growth.
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