What does it mean that God works in mysterious ways?

Sometimes He works actively and obviously — sometimes the finger of God is very manifest (see the finger on the wall in Dan. 5:5). Yet sometimes He acts indirectly in a way we do not immediately detect. He is, so to speak, acting behind the scenes. Yet He is moving the scene. That is what we usually describe as ‘providence’. He is acting in a hidden way.

With the exception of certain solemn judgments on the wicked, and the establishment for a time of His throne in Israel, God's government of the world has, since the entrance of sin, been of a secret, providential character. All things are, indeed, ordered or controlled by divine power; human wickedness is thus checked, and the violence of man's passions restrained; all things are caused to work together for good to God's people; and generally speaking, iniquity becomes, in the long run, its own punishment: but all this is by a mysterious combination and superintendence of events of which natural men know nothing. Faith recognizes it, discerning the hand of God in many things, and confessing it in all; but the world at large neither discern nor own anything but the actual course of events, and the human agencies to which these are attributed. Such is Providence.

Israel or the godly remnant is not in the enjoyment here of covenant blessings, but, when distressed, looks back by faith to a time which recalls the power of Him who cannot change. The comfort of the soul is, that God's way is in the sanctuary, according to the nature and ways of God Himself, so far as He is revealed. If I look out to judge as man, His way is in the sea — I cannot trace it; His footsteps are not known, for who can follow out Him who disposes of all things with a thought? We do know God's own nature and character in relation to us by faith, and can reckon on it, as to all He does, as faithful and unchangeable; but we cannot know and judge His ways in themselves. Hence the unbeliever is discontented and will blame God; the believer is happy, because he has the key to all, in what the God is whom he knows, and on whose ordering of all things he can count. It must be according to what God is. He does not order all things contrary to what He is; but He is for us and therefore orders all things for us — makes all things work together for good. He leads His people like sheep. In Psalm 73 the tried one learned the end of his outward enemies, who prospered while he was chastened. Here he learns the ways of God with himself.

"The mystery of God" (verse 7) is of course the mystery of His ways and dealings with men in relation to their sin. Contemplating more particularly God's ways and judgments with Israel as a nation, the Apostle Paul had to exclaim, "How unsearchable are His judgments, and His ways past finding out!" (Rom. 11:33). What is this but a confession that to the most enlightened of the Lord's servants His ways and judgments are full of mystery. At present God is acting behind the scenes and we cannot penetrate the veil, but when He brings His judgments into the light of day, the mystery of it will vanish away and be finished. What the prophets have declared will be fulfilled, and the rightness of all His dealings through the ages will be seen, as well as of His final judgment at the Second Advent.

The ways of God are intricate, inscrutable, and past finding out, and they are very often perplexing, but how could they be otherwise than mysterious to the finite creature? To any creature they must be simply incomprehensible. If He is pleased to bestow upon us His Holy Spirit that we may understand His wondrous thoughts, that is entirely another matter; and because He has done so our hearts should be filled with thanksgiving, but without the indwelling of that Spirit, which He gives to all who believe on His Son, we could not understand the purposes of His divine mind (1 Cor. 2:9-14). Nothing but the sinful conceit of the human heart would cause anyone to think otherwise.

If the sovereign purposes of God in blessing are worked out, not only in spite of man's failure, but through the very failure of men, we can only say, "O the depth of riches both of the wisdom and knowledge of God". Both the judgments of God in regard to the failure of man, and the ways of God in carrying out His purposes for the blessing of men, make manifest that there are depths of riches in His wisdom and knowledge that are unsearchable, and therefore past finding out by man. If they are to be known, in any measure, it can only be by revelation, and in the practical carrying our of His judgments and ways with men.

His judgments are unsearchable, His ways past finding out: they are impossible to be discovered by all man's ingenuity and searching: He must Himself reveal them if they are to be known at all — nor does this mean that on account of revelation we therefore know everything about His ways. Indeed, how much still we are ignorant of. But He reveals to us what He knows is good for us, and this is sufficient to subdue our hearts with awe when we listen to it aright.

All that lies behind the judgments and the ways of God with His people and with all men of necessity is beyond the comprehension of men, no matter how spiritual or enlightened. God may, on occasion, reveal to His servants what He is about to do, and even give reasons for His actions, as when He spoke to Abraham about the impending destruction of the cities of the plain. Yet how often, after having considered the wisdom and knowledge in the ways of God, we have to exclaim with the apostle, How unsearchable are His judgments and untraceable His ways!

(Vv. 8–11). God’s thoughts and God’s ways are far above man’s legal thoughts and ways, even as the heavens are higher than the earth. God’s blessing, like the rain, comes down from heaven; as with the rain, so with His word, it accomplishes the end for which it is sent.

It was a tremendous set back for Naaman when the prophet sent a messenger out to him, saying "Go and wash in Jordan seven times, and thy flesh shall come again to thee, and thou shalt be clean." This was more than flesh and blood could bear. The Syrian was deeply affronted. As he turned away in rage, he said, "Behold, I thought, he will surely come out to me, and stand, and call on the Name of Jehovah his God, and strike his hand over the place, and recover the leper." We all have our own ideas as to how God should work. But He has said, "MY thoughts are not your thoughts, neither are your ways My ways" (Isa. 55:8). How blessed to come to the end of ourselves, and give up "I thought" once and for ever! The soul only then begins to truly learn.