There are different access routes:
By land access, at kilometer 148 of the Inter-American route there is a sign indicating the crossing to Santa Clara La Laguna and it is that route that is taken to get down to San Juan La Laguna, passing through Santa Clara La Laguna and by San Pablo La Laguna.
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15 Recommendations to get to San Juan La Laguna in your Vehicle from Km. 148 of the Inter-American Route CA-1.
And by water access you can take the boat in Panajachel to San Juan La Laguna.