How do I do a deep copy of a 2d array in Java?

Yes, you should iterate over 2D boolean array in order to deep copy it. Also look at java.util.Arrays#copyOf methods if you are on Java 6.

I would suggest the next code for Java 6:

public static boolean[][] deepCopy(boolean[][] original) {
    if (original == null) {
        return null;
    }

    final boolean[][] result = new boolean[original.length][];
    for (int i = 0; i < original.length; i++) {
        result[i] = Arrays.copyOf(original[i], original[i].length);
        // For Java versions prior to Java 6 use the next:
        // System.arraycopy(original[i], 0, result[i], 0, original[i].length);
    }
    return result;
}

In Java 8 this can be accomplished as a one-liner using lambdas:

<T> T[][] deepCopy(T[][] matrix) {
    return java.util.Arrays.stream(matrix).map(el -> el.clone()).toArray($ -> matrix.clone());
}

I'm a fan of the Arrays utility. It has a copyOf method that will do a deep copy of a 1-D array for you, so you'd want something like this:

//say you have boolean[][] foo;
boolean[][] nv = new boolean[foo.length][foo[0].length];
for (int i = 0; i < nv.length; i++)
     nv[i] = Arrays.copyOf(foo[i], foo[i].length);

I've managed to come up with a recursive array deep copy. It seems to work pretty well even for multi dimensional arrays with varying dimension lengths e.g.

private static final int[][][] INT_3D_ARRAY = {
        {
                {1}
        },
        {
                {2, 3},
                {4, 5}
        },
        {
                {6, 7, 8},
                {9, 10, 11},
                {12, 13, 14}
        }
};

Here is the utility method.

@SuppressWarnings("unchecked")
public static <T> T[] deepCopyOf(T[] array) {

    if (0 >= array.length) return array;

    return (T[]) deepCopyOf(
            array, 
            Array.newInstance(array[0].getClass(), array.length), 
            0);
}

private static Object deepCopyOf(Object array, Object copiedArray, int index) {

    if (index >= Array.getLength(array)) return copiedArray;

    Object element = Array.get(array, index);

    if (element.getClass().isArray()) {

        Array.set(copiedArray, index, deepCopyOf(
                element,
                Array.newInstance(
                        element.getClass().getComponentType(),
                        Array.getLength(element)),
                0));

    } else {

        Array.set(copiedArray, index, element);
    }

    return deepCopyOf(array, copiedArray, ++index);
}

EDIT: Updated the code to work with primitive arrays.

Yes, that's the only way to do it. Neither java.util.Arrays not commons-lang offer deep copy for arrays.